The revised rules, which went into effect Monday, double the fines for illegal fishing to 200 million won (US$173,000) from 100 million won, the Ministry for Food, Agriculture, Forestry and Fisheries said.
Under the new guidelines, any boat that fails to stop when ordered to do so by South Korea's fisheries authorities or the Coast Guard can also be fined 100 million won, up from the current 50 million won, reports YonhapNewsAgency.
Fishing boats that enter South Korea's territorial waters to fish without proper permits or use force to resist inspection or arrest will be subject to aggravated punishment in addition to fines.
Such punishment will entail the confiscation of all fishing tools, such as nets, and any catch in the boat's hold.
"By sharply raising the maximum limit of fines and enforcing other punitive measures, Seoul hopes to discourage illegal fishing in its EEZ, which has become endemic and threatens to deplete the country's marine resources," a ministry official said.
Almost all illegal fishing within South Korea's EEZ is by Chinese fishing boats.
As fishermen will try to evade being caught for fear of paying stiffer fines, the official said, greater cooperation will take place between fisheries authorities, the Coast Guard and the Navy.